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While the Pauli-$Z$ matrix is a 2 x 2 matrix, there are more basis states that need to be considered, namely the vacuum. The atomic basis states are $\left|0\right>$ and $\left|1\right>$, representing the number of excitations in the atom (as it's only a two-level atom, there can't be more than 1 excitation) and this is what $Z$ acts on. Similarly, the ...

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